Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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  • See Evidence submitted by expert panel for details.

Variant: NM_000314.6(PTEN):c.-975G>A

CA000653

127684 (ClinVar)

Gene: PTEN
Condition: PTEN hamartoma tumor syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 0a3b6aa8-ca64-4f5b-bf58-e79930be9a9f
Approved on: 2019-11-22
Published on: 2019-12-04

HGVS expressions

NM_000314.6(PTEN):c.-975G>A
NC_000010.11:g.87863494G>A
CM000672.2:g.87863494G>A
NC_000010.10:g.89623251G>A
CM000672.1:g.89623251G>A
NC_000010.9:g.89613231G>A
NG_007466.2:g.5057G>A
NG_033079.1:g.4944C>T
NM_000314.5:c.-975G>A
NM_000314.6:c.-975G>A
NM_001304717.2:c.-456G>A
NM_001304718.1:c.-1680G>A
ENST00000371953.7:c.-976G>A
ENST00000610634.1:c.-1078G>A

Likely Benign

Met criteria codes 2
BS1 BS2_Supporting
Not Met criteria codes 20
PP2 PP3 PP1 BA1 PM2 PM6 PM5 PM4 PM1 BS3 BS4 PS1 PS3 PS4 PS2 BP7 BP5 BP2 BP4 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.-975G>A (NC_000010.10:g.89623251G>A) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). BS1: Allele frequency of 0.00127 (0.127%, 11/8660 alleles) in the African subpopulation of the gnomAD cohort. (PMID 27535533) BS2_P: Meets criteria for BS2 (observed in the homozygous state in at least one healthy or PHTS-unaffected individual) but BS1 is also applied. (internal laboratory contributor ClinVar Organization ID: 61756)
Met criteria codes
BS1
0.127% in African subpop of gnomAD (11/8660 alleles)
BS2_Supporting
2 Ambry cases: 1 breast dx 30 mother HET; 1 unaffected F in 40s, no confirmation. BS2_P approved during EP review.
Not Met criteria codes
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
Eng lab data: one family (proband ID 9151) demonstrating lack of segregation, another (proband ID 9898) with 1 meiosis, family #3 (proband ID 763) non-contributory.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
N/A since BS1 applies
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
2 GDx internal cases with other PATH variants phase unk. One more required for BP2.
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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